2007
DOI: 10.1089/cmb.2007.r018
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Biological Networks: Comparison, Conservation, and Evolution via Relative Description Length

Abstract: We describe a new approach for comparing cellular-biological networks and finding conserved regions in two or more such networks. Our distance measure is based on the description length of one network, given the description of the other one, and it is efficiently computable. We employ these distances as inputs for generating phylogenetic trees. Using KEGG's metabolic networks as our starting point, we obtained trees that are not perfect, but are very good (considering the characteristics of the inputs). Our ap… Show more

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Cited by 12 publications
(4 citation statements)
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“…When those individuals are species and the relation is the sequence similarity of their genomes, the tree-like representation becomes a phylogenetic tree. Phylogenetic trees can also be inferred from metabolic pathways (Forst and Schulten, 2001 ; Chor and Tuller, 2007 ), protein–protein interaction networks (Erten et al, 2009 ), tumor clones of cancer (Miura et al, 2020 ), languages (Pompei et al, 2011 ), music (Bomin et al, 2016 ), etc., with appropriate distance or similarity relations. At the beginning, phylogenetic trees were designed to infer evolutionary relationships based on some species appearance (mainly morphological and physiological traits).…”
Section: Introductionmentioning
confidence: 99%
“…When those individuals are species and the relation is the sequence similarity of their genomes, the tree-like representation becomes a phylogenetic tree. Phylogenetic trees can also be inferred from metabolic pathways (Forst and Schulten, 2001 ; Chor and Tuller, 2007 ), protein–protein interaction networks (Erten et al, 2009 ), tumor clones of cancer (Miura et al, 2020 ), languages (Pompei et al, 2011 ), music (Bomin et al, 2016 ), etc., with appropriate distance or similarity relations. At the beginning, phylogenetic trees were designed to infer evolutionary relationships based on some species appearance (mainly morphological and physiological traits).…”
Section: Introductionmentioning
confidence: 99%
“…Yet, a lot of conjectures exist in the literature regarding the presence of traces of evolution at the level of the PINs. Even though evolution is usually studied at the genomics level, a sizeable number of researchers claim and support that there must also be an obvious presence of species divergence at the level of the PINs 6,11,12 .…”
Section: Introductionmentioning
confidence: 99%
“…Analogous to sequence alignment which identifies conserved sequences, network alignment reveals connectivity patterns that are conserved among two or more organisms. A number of studies have been done to systematically align different types of biological networks [1][2][3][4][5][6][7][8][12][13][14][15][16][17]. For metabolic networks, Pinter et al [20] devised an algorithm that aligns query networks with specific topologies by using a graph theoretic approach.…”
Section: Introductionmentioning
confidence: 99%